On a whim I reinstalled gksu and this seems to have fixed my problem.
** Changed in: synaptic (Ubuntu)
Status: New => Fix Committed
** Changed in: synaptic (Ubuntu)
Assignee: (unassigned) => Marion Smith (msmith-extremeprogrammers)
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Synaptic Not Prompting For Password/Hangs
https://bugs.launchpad.net/bugs/402781
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